Award-Winning Animation Helps Scientists See Nature at Work

August 8, 2008

NREL senior scientist Michael Crowley and his animation of an enzyme molecule, which
was awarded second place in the Department of Energy's Electronic Visualization competition.

Its official name is cellobiohydrolase Cel7A. In Michael Crowley's award-winning animated
version, it looks a Technicolor dinosaur fossil chomping on dinner.

In reality, Cel7A is just the opposite – it's a vegetarian molecule that is nature's
primary agent for decaying plants. Crowley, an NREL senior scientist, and his associates
are modeling Cel7A in hopes of bioengineering a version that will accelerate the process
of making cellulosic ethanol from woody plants and farm wastes. A breakthrough like
this would enable biofuels to be produced more easily from abundant biomass wastes
and could reduce our nation's dependence on foreign oil.

What makes the award especially noteworthy is the nature of the competition. His animation
was one of 52 submissions by national laboratories and universities. Nearly all of
the contestants were visualizing the behavior of large-scale phenomenon – the top
prize went to a visualization of Hurricane Katrina.

Visualizing a Single Molecule

Crowley's work focuses on the behavior of a single, very important molecule. While
something like a storm model can become very large, it can be divided into discrete
sections and follows a logical sequence.

In contrast, Crowley said, animating Cel7A required finding ways to successfully model
the interactivity of many atoms interacting dynamically with each other – simultaneously.

"It is very difficult to parallelize the process to run even on a huge computer,"
Crowley said. "We're dealing with one molecule, but a lot of atoms and they're all
talking to each other. Even if you have 1,000 processors, it's not easy to speed up."

Crowley is a Long Island native. He studied chemistry as an undergraduate at Fordham
University and received a Ph.D. from the University of Montana. He most recently
worked at The Scripps Research Institute in La Jolla, Calif., where he studied protein
folding in human metabolism and helped develop high performance computer programming.
He joined NREL 16 months ago and started his own high performance computer group after
consulting with the laboratory's biofuels program. Read more about Michael Crowley and access his publications.

It's All About Metabolism

Now Crowley is investigating an enzyme found in fungi and termite guts that breaks
down the tough complex carbohydrates in plant cell walls and turns them into a simpler
form of sugar. To him, it's still all about metabolism.

In nature, that sugar is food for the termite or other organisms. At NREL, it becomes
the material that is more easily refined into biofuels.

By using cellulose, refiners could make large quantities of ethanol from the widely
available leftovers from agriculture and forestry rather than using edible corn and
other grains.

While Cel7A does its catalytic job well in nature – it produces one unit of simple
sugar per second – it would have to work much faster to convert enough cellulose to
expand liquid biofuels into an affordable choice at the pump.

Changing it won't be easy. The same biochemical and structural factors that make plants
resilient in nature make them difficult to break down for fuels.

Visualizing the enzyme's process on the submolecular scale could help NREL scientists
to see opportunities where they might re-engineer the enzyme – perhaps by combining
it with elements of different enzymes that work faster.

The goal: double the molecule's output of simple sugars to a pair of units per second.

"Visually, our brains can recognize patterns very quickly," Crowley said. "We can
look at an animation and see what is different or what is wrong very quickly. We can
sample that region of the enzyme, analyze it, and get the real science out of it."